mapcomp-all: Functions for comparison of two map orders

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Takes in two maps with the aim of comparing the position of common markers. Creates a mapcomp object for plotting and summary.

Usage

mapcomp(object1, object2)

## S3 method for class 'mapcomp'
plot(x, lines = FALSE, ...)

## S3 method for class 'mapcomp'
summary(object, ...)

Arguments

object1	Object inheriting class mpcross or class map
object2	Object inheriting class mpcross or class map
x	Object of class mapcomp
lines	Whether straight lines with slope +1 / -1 (indicating complete map agreement) should be shown
...	Additional arguments
object	Object of class mapcomp for summarizing

Value

An object of class mapcomp with components:

commonmrk	A matrix containing 5 columns with the names of all common markers for the two maps (mname), the chromosome mapped to in the first map (chr1), the position mapped to in the first map (pos1), the chromosome mapped to in the second map (chr2) and the position mapped to in the second map (pos2)
samechr	A matrix containing 5 columns as above. Differs from commonmrk in that duplicated markers in either map will have been removed, so all markers map to exactly one chromosome
map1	The first map - either the originally input object1, or object1$map if it inherits class mpcross
map2	The first map - either the originally input object2, or object2$map if it inherits class mpcross
correlations	The correlation between positions in map1 and map2 for each chromosome
dup1	The names of markers duplicated in map1
dup2	The names of markers duplicated in map2

Plot produces for a comparison for each chromosome of positions of markers which are mapped to that chromosome in both maps

Summary function returns printed summary including - number of markers in each map; number of markers common to both maps; number of duplicated markers in each map; number of markers mapped to different chromosomes; correlations between positions on each chromosome.

Examples

map1 <- qtl::sim.map(len=rep(100, 4), n.mar=51, include.x=FALSE)
map2 <- qtl::sim.map(len=rep(100, 4), n.mar=51, include.x=FALSE)
mc <- mapcomp(map1, map2)
summary(mc)
plot(mc)

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.